I'd have to look at the specific cases they're talking about. I'm not sure the answer to the very specific question: are there cases where this has been done and allowed? I'd be surprised if there were, unless there was a very specific instance.
I can also say that that section is not new. That section has been there since the 1920s. The idea is that a fundamental principle of fisheries protection is ensuring safe fish passage. That section means to speak to safe fish passage, so that you can't put a net across a river and catch all the fish that are going down.
There may be some very specific purposes under which we might have done it in the past, or it might have been allowed in the past, but I think that section is meant to be in there. It's been there since the twenties and we've used it in terms of fisheries management.